use sequera containers for download_assemblies

Author: Zachary Foster

conf/modules.config

@@ -389,6 +389,8 @@ process {
     }
 
     withName: 'MAIN_REPORT.*' {
+        // Logs indicate this process can some time use a large amount of swap for an unknown reason, so this prevents that
+        containerOptions = { workflow.containerEngine == 'singularity' ? '' : "--memory-swap ${task.memory.mega.intValue()}m" }
         publishDir = [
             path: { "${params.outdir}/reports" },
             mode: params.publish_dir_mode,

modules/local/download_assemblies/main.nf

@@ -4,8 +4,8 @@ process DOWNLOAD_ASSEMBLIES {
 
     conda "conda-forge::ncbi-datasets-cli=15.11.0 bioconda::samtools=1.18 conda-forge::unzip=6.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'quay.io/nf-core/ncbi-datasets-cli:0.1':
-        'quay.io/nf-core/ncbi-datasets-cli:0.1' }"
+        'community.wave.seqera.io/library/samtools_ncbi-datasets-cli_unzip:155f739985f03f20':
+        'community.wave.seqera.io/library/samtools_ncbi-datasets-cli_unzip:155f739985f03f20' }"
 
     input:
     tuple val(ref_meta), val(id)